"Missing Shipment" was renamed "The Peddler's Fate" a while back, you're playing an older version. The current one is v3.12, with another update due in the next 2-3 weeks or so.
Regarding your specific comments:
1) The game explores a lot of kinks & fetishes. A LOT. No one expects any particular player to find all of that content appealing.
2) Some Side quests have to be completed before certain Main quests are available, but any additional quests in that storyline don't have to be done. For example you need to get Rosy's bakery up and running but don't have to pursue her storyline past that.
3) You don't have to peep on Beth at all, let alone get the spyglass. I made that mistake myself. Just get her Affection high enough (though she only agrees to a date with you after Restore The Temple is done). It's a lot of shoveling, but it works.
4) You do not have to return to Maghda (the ogress) after that first time, but you need to get Edgar's stuff back so he can open his shop. You'll be buying outfits from him even if you avoid as many side quests as you can. That includes Main quests...you have to complete Shopping (for Erevi in the Tower) before Restore The Temple is available.
5) Goblins are a recurring threat. They were nearly wiped out 20 years ago and now they're back. You can't reduce their threat without following their quests. If you don't, you accept they will continue to be an issue in the game. (The goblins questline is extremely popular, thouh.)
Other Side questlines don't have to be done at all. For example you can complete the game having done zero content for Mia, Victoria, Alice, the giants, or the goblins (and this list is incomplete...). However, nearly all the Side girls' questlines provide some kind of in-game benefit if you follow them. Passive income, access to more ingredients, the ability to buy things you normally can't buy, etc.